Shred the onions and jalapeno peppers in a food processor, using the shredding blade.
Combine the onion, jalapeno pepper, vinegar, black pepper, and salt in a large pot and place over medium heat. Stirring frequently, bring to a full boil; cook for 10 minutes.
Pack the mixture firmly into sterilized pint canning jars to within 3/4 inch of the top. Pour the cooking liquid over the onions to within 1/2 inch of the top and using a spatula, stir gently to remove all air bubbles. Wipe the rims with a clean damp cloth and adjust lids and rings firmly. Process in a boiling water bath for five minutes.